342 lines
14 KiB
Java
342 lines
14 KiB
Java
package eu.dnetlib.dhp.bypassactionset;
|
|
|
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
import eu.dnetlib.dhp.bypassactionset.fos.PrepareFOSSparkJob;
|
|
import eu.dnetlib.dhp.bypassactionset.fos.GetFOSData;
|
|
import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
|
|
import eu.dnetlib.dhp.common.collection.CollectorException;
|
|
import eu.dnetlib.dhp.countrypropagation.CountryPropagationJobTest;
|
|
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
|
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
|
import org.apache.commons.io.FileUtils;
|
|
import org.apache.hadoop.conf.Configuration;
|
|
import org.apache.hadoop.fs.FileSystem;
|
|
import org.apache.hadoop.fs.LocalFileSystem;
|
|
|
|
import java.nio.file.Path;
|
|
import org.apache.spark.SparkConf;
|
|
import org.apache.spark.api.java.JavaRDD;
|
|
import org.apache.spark.api.java.JavaSparkContext;
|
|
import org.apache.spark.sql.SparkSession;
|
|
import org.junit.jupiter.api.AfterAll;
|
|
import org.junit.jupiter.api.BeforeAll;
|
|
import org.junit.jupiter.api.Test;
|
|
import org.slf4j.Logger;
|
|
import org.slf4j.LoggerFactory;
|
|
|
|
import java.io.BufferedReader;
|
|
import java.io.IOException;
|
|
import java.io.InputStreamReader;
|
|
import java.nio.file.Files;
|
|
|
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
|
import static org.junit.jupiter.api.Assertions.assertTrue;
|
|
|
|
public class GetFOSTest {
|
|
private static final Logger log = LoggerFactory.getLogger(GetFOSTest.class);
|
|
|
|
private static Path workingDir;
|
|
private static SparkSession spark;
|
|
private static LocalFileSystem fs;
|
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
|
private static final String ID_PREFIX = "50|doi_________";
|
|
|
|
@BeforeAll
|
|
public static void beforeAll() throws IOException {
|
|
workingDir = Files.createTempDirectory(CountryPropagationJobTest.class.getSimpleName());
|
|
|
|
fs = FileSystem.getLocal(new Configuration());
|
|
log.info("using work dir {}", workingDir);
|
|
|
|
SparkConf conf = new SparkConf();
|
|
conf.setAppName(GetFOSTest.class.getSimpleName());
|
|
|
|
conf.setMaster("local[*]");
|
|
conf.set("spark.driver.host", "localhost");
|
|
conf.set("hive.metastore.local", "true");
|
|
conf.set("spark.ui.enabled", "false");
|
|
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
|
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
|
|
|
spark = SparkSession
|
|
.builder()
|
|
.appName(CountryPropagationJobTest.class.getSimpleName())
|
|
.config(conf)
|
|
.getOrCreate();
|
|
}
|
|
@AfterAll
|
|
public static void afterAll() throws IOException {
|
|
FileUtils.deleteDirectory(workingDir.toFile());
|
|
spark.stop();
|
|
}
|
|
|
|
|
|
@Test
|
|
void getFOSFileTest() throws CollectorException, IOException, ClassNotFoundException {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/h2020_fos_sbs.csv")
|
|
.getPath();
|
|
final String outputPath = workingDir.toString() + "/fos.json";
|
|
|
|
|
|
|
|
|
|
new GetFOSData()
|
|
.doRewrite(sourcePath, outputPath, "eu.dnetlib.dhp.bypassactionset.FOSDataModel", '\t',fs );
|
|
|
|
BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
|
|
|
|
String line;
|
|
int count = 0;
|
|
while ((line = in.readLine()) != null) {
|
|
FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
|
|
|
|
System.out.println(new ObjectMapper().writeValueAsString(fos));
|
|
count += 1;
|
|
}
|
|
|
|
assertEquals(38, count);
|
|
|
|
|
|
}
|
|
|
|
|
|
@Test
|
|
void distributeDoiTest() throws Exception{
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos.json")
|
|
.getPath();
|
|
|
|
PrepareFOSSparkJob
|
|
.main(
|
|
new String[] {
|
|
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"--sourcePath", sourcePath,
|
|
|
|
"-outputPath", workingDir.toString() + "/distribute"
|
|
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<FOSDataModel> tmp = sc
|
|
.textFile(workingDir.toString() + "/distribute")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
|
|
|
|
String doi1 = ID_PREFIX +
|
|
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.3390/s18072310"));
|
|
|
|
assertEquals(50, tmp.count());
|
|
assertEquals(1, tmp.filter(row -> row.getDoi().equals(doi1)).count());
|
|
assertEquals("engineering and technology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel1());
|
|
assertEquals("nano-technology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel2());
|
|
assertEquals("nanoscience & nanotechnology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel3());
|
|
|
|
String doi = ID_PREFIX +
|
|
IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/1365-2656.12831"));
|
|
assertEquals(1, tmp.filter(row -> row.getDoi().equals(doi)).count());
|
|
assertEquals("social sciences", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel1());
|
|
assertEquals("psychology and cognitive sciences", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel2());
|
|
assertEquals("NULL", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel3());
|
|
|
|
// {"doi":"10.1111/1365-2656.12831\u000210.17863/cam.24369","level1":"social sciences","level2":"psychology and cognitive sciences","level3":"NULL"}
|
|
|
|
}
|
|
|
|
/**
|
|
* @Test
|
|
* void testCountryPropagationSoftware() throws Exception {
|
|
* final String sourcePath = getClass()
|
|
* .getResource("/eu/dnetlib/dhp/countrypropagation/sample/software")
|
|
* .getPath();
|
|
* final String preparedInfoPath = getClass()
|
|
* .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo")
|
|
* .getPath();
|
|
* SparkCountryPropagationJob
|
|
* .main(
|
|
* new String[] {
|
|
* "--isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
* "--sourcePath", sourcePath,
|
|
* "-saveGraph", "true",
|
|
* "-resultTableName", Software.class.getCanonicalName(),
|
|
* "-outputPath", workingDir.toString() + "/software",
|
|
* "-preparedInfoPath", preparedInfoPath
|
|
* });
|
|
*
|
|
* final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
*
|
|
* JavaRDD<Software> tmp = sc
|
|
* .textFile(workingDir.toString() + "/software")
|
|
* .map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
|
*
|
|
* // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
|
|
*
|
|
* Assertions.assertEquals(10, tmp.count());
|
|
*
|
|
* Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
|
|
*
|
|
* Assertions.assertEquals(6, verificationDs.filter("size(country) > 0").count());
|
|
* Assertions.assertEquals(3, verificationDs.filter("size(country) = 1").count());
|
|
* Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count());
|
|
* Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count());
|
|
*
|
|
* Dataset<String> countryExploded = verificationDs
|
|
* .flatMap(
|
|
* (FlatMapFunction<Software, Country>) row -> row.getCountry().iterator(), Encoders.bean(Country.class))
|
|
* .map((MapFunction<Country, String>) Qualifier::getClassid, Encoders.STRING());
|
|
*
|
|
* Assertions.assertEquals(9, countryExploded.count());
|
|
*
|
|
* Assertions.assertEquals(1, countryExploded.filter("value = 'FR'").count());
|
|
* Assertions.assertEquals(1, countryExploded.filter("value = 'TR'").count());
|
|
* Assertions.assertEquals(2, countryExploded.filter("value = 'IT'").count());
|
|
* Assertions.assertEquals(1, countryExploded.filter("value = 'US'").count());
|
|
* Assertions.assertEquals(1, countryExploded.filter("value = 'MX'").count());
|
|
* Assertions.assertEquals(1, countryExploded.filter("value = 'CH'").count());
|
|
* Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count());
|
|
*
|
|
* Dataset<Tuple2<String, String>> countryExplodedWithCountryclassid = verificationDs
|
|
* .flatMap((FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
* List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
* List<Country> countryList = row.getCountry();
|
|
* countryList
|
|
* .forEach(
|
|
* c -> prova
|
|
* .add(
|
|
* new Tuple2<>(
|
|
* row.getId(), c.getClassid())));
|
|
* return prova.iterator();
|
|
* }, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
*
|
|
* Assertions.assertEquals(9, countryExplodedWithCountryclassid.count());
|
|
*
|
|
* countryExplodedWithCountryclassid.show(false);
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 1,
|
|
* countryExplodedWithCountryclassid
|
|
* .filter(
|
|
* "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'FR' ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 1,
|
|
* countryExplodedWithCountryclassid
|
|
* .filter(
|
|
* "_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'TR' ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 2,
|
|
* countryExplodedWithCountryclassid
|
|
* .filter(
|
|
* "_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'IT' or _2 = 'MX') ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 2,
|
|
* countryExplodedWithCountryclassid
|
|
* .filter(
|
|
* "_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'IT' or _2 = 'US') ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 1,
|
|
* countryExplodedWithCountryclassid
|
|
* .filter(
|
|
* "_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'JP'")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 2,
|
|
* countryExplodedWithCountryclassid
|
|
* .filter(
|
|
* "_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'CH' or _2 = 'JP') ")
|
|
* .count());
|
|
*
|
|
* Dataset<Tuple2<String, String>> countryExplodedWithCountryclassname = verificationDs
|
|
* .flatMap(
|
|
* (FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
* List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
* List<Country> countryList = row.getCountry();
|
|
* countryList
|
|
* .forEach(
|
|
* c -> prova
|
|
* .add(
|
|
* new Tuple2<>(
|
|
* row.getId(),
|
|
* c.getClassname())));
|
|
* return prova.iterator();
|
|
* },
|
|
* Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
*
|
|
* countryExplodedWithCountryclassname.show(false);
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 1,
|
|
* countryExplodedWithCountryclassname
|
|
* .filter(
|
|
* "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 1,
|
|
* countryExplodedWithCountryclassname
|
|
* .filter(
|
|
* "_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'Turkey' ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 2,
|
|
* countryExplodedWithCountryclassname
|
|
* .filter(
|
|
* "_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'Italy' or _2 = 'Mexico') ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 2,
|
|
* countryExplodedWithCountryclassname
|
|
* .filter(
|
|
* "_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'Italy' or _2 = 'United States') ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 1,
|
|
* countryExplodedWithCountryclassname
|
|
* .filter(
|
|
* "_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'Japan' ")
|
|
* .count());
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 2,
|
|
* countryExplodedWithCountryclassname
|
|
* .filter(
|
|
* "_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'Switzerland' or _2 = 'Japan') ")
|
|
* .count());
|
|
*
|
|
* Dataset<Tuple2<String, String>> countryExplodedWithCountryProvenance = verificationDs
|
|
* .flatMap(
|
|
* (FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
* List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
* List<Country> countryList = row.getCountry();
|
|
* countryList
|
|
* .forEach(
|
|
* c -> prova
|
|
* .add(
|
|
* new Tuple2<>(
|
|
* row.getId(),
|
|
* c
|
|
* .getDataInfo()
|
|
* .getInferenceprovenance())));
|
|
* return prova.iterator();
|
|
* },
|
|
* Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
*
|
|
* Assertions
|
|
* .assertEquals(
|
|
* 7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
|
|
* }
|
|
*/
|
|
}
|